New features in version 2.1:

2.0 was the last major version of Pratt, in the 2.1 version only minor things
have been added/changed. A few bugs in version 2.0 have been fixed in 2.1.
Inge Jonassen is grateful to Dr. John F. Collins, University of Edinburgh,
who proposed many of the added features, and discovered many of the bugs.

Command line search control -- the user can now choose values for all parameters
that are in the menu directly from the command line.
This makes it quicker for experienced user to specify his/her search, and
also makes it easier to call Pratt from inside other programs.

When showing the sequence segments matching each pattern, the sequence symbols matching
non-wildcard positions (components) in the pattern, are written in upper-case while
sequence symbols matching wild-cards are in lower-case. Also, gaps (-) are added to
align the symbols matching each pattern component.

On-line help is available from the menu by typing "help <option>"
where option is one of the options in the menu or help for general
help about Pratt.

Summary information about where the patterns match in the sequences is written
horizontally or vertically.

The user can restrict where in the sequences patterns should be looked for.
This can be useful for example if the user knows some constraints on the position
of the patterns in one or more of the sequences.

When using Pratt interactively (using the menu), some summary information
about the search parameters will be shown after the user asks the search
to be started, and the user is given the opportunity to go back to the
menu to change parameter values.

What was new in version 2.0?

In addition to the set S of protein sequences, the user
can input:

A multiple sequence alignment of some of the sequences in S,
or of all sequences in S, and Pratt will search
only for patterns consistent with the alignment.

Input a special query sequence, and Pratt will search only
for patterns matching this sequence and some propotion of the
other sequences.

Branch-and-bound and heuristics have been added to make the pattern
search more efficient. The speed-up is significant, in particular for
sets of relatively similar (closely related) sequences.

Pratt has integrated new pattern scoring mechanisms, including one taking
into account the diversity of the sequences matching a pattern, and another
taking into account the number of sequences matching each pattern.

1. What is Pratt?

Pratt is a tool that allows the user to search for patterns conserved in a set
of protein sequences. The user can specify what kind of patterns
should be searched for, and how many sequences should match a
pattern to be reported.

1.2 Pattern terminology

The patterns that can be found is a subset of the set of patterns
that can be described using Prosite notation.

A pattern that can be found by Pratt can be written on the form

A(1)-x(i1,j1)-A2-x(i2,j2)-....A{p-1}-x(i{p-1},j{p-1})-Ap
where

A(k) is a component of the pattern, either specifying one
amino acid, e.g. C, or a set of amino acids, e.g. [ILVF].
A pattern component A(k) is an

identity component

if it specifies exactly one amino acid (for instance C or L),

ambiguous component

if it specifies more than one (for instance [ILVF] or [FWY]).

i(k), j(k) are integers so that i(k)<=j(k) for all k. The part
x(ik,jk) specifies a wildcard region of the pattern matching
between ik and jk arbitrary amino acids.
A wildcard region x(ik,jk) is

flexible

if jk is bigger than ik (for example x(2,3).
The flexibility of such a region is jk-ik.br>
For example the flexibility of x(2,3) is 1.

fixed

if j(k) is equal to i(k), e.g., x(2,2) which can be written as x(2).

The product of flexibility for a pattern is the product of the
flexibilities of the flexible wildcard regions in the pattern,
if any, otherwise it is defined to be one.

Examples:

C-x(2)-H is a pattern with two components (C and H) and one fixed
wildcard region. It matches any sequence containing a C followed
by any two arbitrary amino acids followed by an H.
For example aaChgHyw and liChgHlyw.

C-x(2,3)-H is a pattern with two components (C and H) and one
flexible wildcard region. It matches any sequence containing a
C followed by any two or three arbitrary amino acids followed
by an H.
For example aaChgHywk and liChgaHlyw.

C-x(2,3)-[ILV] is a pattern with two components (C and [ILV])
and one flexible wildcard region. It matches any sequence containing
a C followed by any two or three arbitrary amino acids followed
by an I, L or V.

2. User manual.

2.1 Format of input sequences.

Make a file or a set of files containing the set of sequences to be
analysed. Currently, Pratt can read one of the formats:

Fasta format. One file containing all the sequences. One sequence
is specified by

one line starting with '>' in position 1 and then the name of the
sequence, and

some lines containging the sequence in upper or lower case.
The end of a sequence is identified by looking for either the
start of a new sequence or the end of the file.

Pratt does not allow for annotation in FastA format input files.

SWISS-PROT format. One file containing all the sequences. One sequence
is specified by

one line starting with 'ID' and then the name of the sequence,
followed by an arbitrary number of lines, and then

a line starting with 'SQ' (rest of the line ignored), followed by
the sequence (on one or several lines), followed by a line starting
with '//'

2.2 Command line.

Command line:

Pratt <format> <filename> [options]

where <format> is one of fasta swissprot
and <filename> is
the name of a file containing the sequences in the given format

2.3 Using the menu to control your search.

When you run Pratt, it will give you a menu allowing you to set a variety of
parameters controlling:

what kind of patterns Pratt is going to look for,

how many sequences a pattern should match,

lower threshold on significance for a pattern to be reported, and

how many patterns should be reported.

greediness in search (new in version 2.0)

if a query sequence or an alignment is to be used (new in version 2.0)

if a pattern is restricted to match within a specified region in one or several
of the sequences (new in version 2.1).

Schematic figure of algorithm used in Pratt version 2.x

Overview of the pattern discovery algorithm.
The user inputs a set unaligned sequences, and the minimum
number of sequences to match a pattern.
(i):
During this phase, patterns are constrained to the pattern class
defined by the bounds set using the menu.
A pattern graph can be constructed either
from the shortest sequences in S (1),
from a special query sequence (2), or
from a multiple sequence alignment (3).
A search is done for the highest scoring patterns in the class
that can be derived from the pattern graph.
The block data structure is used to find all matches to each pattern.
(ii):
The highest scoring patterns found during this search, are input to a
heuristic pattern refinement algorithm, where more ambiguous pattern
components (from a list given by the user in Pratt.sets) can be
added to the patterns found during phase (i).
The refinement phase is optional.

The C parameters control how many sequences a pattern should match to
be considered by Pratt:

CM:

Set the minimum number of sequences to match a pattern.
Pratt will only report patterns that match at least the chosen
number of the sequences that you have input. Pratt will not allow
you to choose a value higher than the number of sequences input.

C%:

set the minimum percentage of the input sequences that should match a pattern.
If you set this to, say 80, Pratt will only report patterns
matching at least 80 % of the sequences input.

G Options:

Allows the use of an alignment or a query sequence to restrict the pattern search.

If G is set to al or query, another option GF will appear
allowing the user to give the name of a file containing a
multiple sequence alignment (in Clustal W format), or a
query sequence in FastA format (without annotation).n
Only patterns consistent with the alignment/matching the query
sequence will be considered.

Loosely a pattern is considered consistent with the alignment if

each symbol in the pattern (e.g. A) corresponds to a ungapped column
in the alignment where all the characters match the pattern symbol
(in the example, A).

the wildcards in the pattern are compatible with the number of
residues between the corresponding columns in the alignment.

For instance the pattern A-x(2,3)-B is consistent with the alignment

ALVGB
AG-LB
ALD-B

For more details see
I. Jonassen Efficient discovery of conserved patterns using a pattern graph.
Submitted to CABIOS

B Options:

Using the B options (BN,BI,BF) on the menu you can control which
pattern symbols will be used during the initial pattern
search and during the refinement phase.
In the pattern C-x(2)-[DE], C and [DE] are the symbols.

The pattern symbols that can be used, are read from a file
if the BI option is set, otherwise a default set will be used.

The default set has as the 20 first elements, the single amino acid
symbols, and it also contains a set of ambiguous symbols, each
containing amino acids that share some physio-chemical properties

If BI is set, option BF will appear to allow you to give the
name of the file. In the file each symbol is given on a separate
line contatining the letters that the symbol should match.
For instance the file could be:

C
DE

and only patterns with the symbols C and [DE] would
be considered. During the initial search, pattern symbols
corresponding to the first BN lines can be used.
Increasing BN will slow down the search and increase the
memory usage, but allow more ambiguous pattern symbols.

P Options:

The P options are for controlling the patterns to be considered
by Pratt. See also the F options for controlling flexibility.

Option PL:

allows you to set the maximum length of a pattern.
The length of the pattern C-x(2,4)-[DE] is 1+4+1=6.
The memory requirement of Pratt depends on L; a higher L
value gives higher memory requirement.

Option PN:

using this you can set the maximum number of symbols
in a pattern. The pattern C-x(2,4)-[DE] has 2 symbols (C and [DE]).
When PN is increased, Pratt will require more memory.

Option PX:

Using this option you can set the maximum length of a
wildcard. Examples of wildcards and lengths are

x - 1
x(10) - 10
x(3,4) - 4

Increasing PX will increase the time used by Pratt,
and also slightly the memory required.

F Options:

The F options control flexible wildcards in the patterns:

Option FN:

Using this option you can set the maximum number of
flexible wildcards (matching a variable number of
arbitrary sequence symbols). For instance x(2,4)
is a flexible wildcard, and the pattern

C-x(2,4)-[DE]-x(10)-F

contains one flexible wildcard.

Increasing FN will increase the time used by Pratt.

Option FL:

you can set the maximum flexibility of
a flexible wildcard (matching a variable number of
arbitrary sequence symbols). For instance x(2,4) and
x(10,12) has flexibility 2, and x(10) has flexibility 0.
Increasing FL will increase the time used by Pratt.

Option FP:

Using option FP you can set an upper limit on the product
of a flexibilities for a pattern. This is related to
the memory requirements of the search, and increasing
the limit, increases the memory usage.
Some patterns and the corresponding product of flexibilities:

Using the E parameter you can adjust the greediness of the
search. Setting E to 0 (zero), the search will be exhaustive.
Increasing E increases the greediness, and decreases the time
used in the search.

Option R:

When the R option is switched on, patterns found during the
initial pattern search are input to a refinement algorithm
where more ambiguous pattern symbols can be added.

For instance the pattern

C-x(4)-D

might be refined to

C-x-[ILV]-x-D-x(3)-[DEF]

If the RG option is switched on, then ambiguous symbols listed in the
symbols file (or in the default symbol set -- see help for option B),
are used. If RG is off, only the letters needed to match the input
sequences are inlcuded in the ambiguous pattern positions.

For example, if [ILV] is a listed allowed symbol, and [IL] is not, [IL] can
be included in a pattern if RG is off, but if RG is on, the full symbol
[ILV] will be included instead.

O Options:

The O options allow you to control the output from Pratt:

Option OF:

allows you to specify the name of the file to
which Pratt will write its output

set the max. nr of patterns for which Pratt is to
produce an alignment of the sequence segments matching it.

M Options:

If the M option is set, then Pratt will print out the location
of the sequence segments matching each of the (maximum 52) best
patterns. The patterns are given labels A, B,...Z,a,b,...z in order
of decreasing pattern score. Each sequence is printed on a line,
one character per K-tuple in the sequence. If pattern with label C
matches the third K-tuple in a sequence C is printed out. If several
patterns match in the same K-tuple, only the best will be printed.

Option MR:

sets the K value (ratio) used for printing the summary
information about where in each sequence the pattern matches are found.

Option MV:

if set, the output is printed vertically instead of horizontally,
vertical output can be better for large sequence sets.

S Options:

The S option allows you to control the scoring of patterns.
There are five possible scoring schemes to be used:

info

patterns are scored by their information content as defined in
(Jonassen et al, 1995). Note that a pattern's score is independent
of which sequences it matches.

mdl

patterns are scored by a Minimum Description Length principle
derived scoring scheme, which is related to the one above, but
penalises patterns scoring few sequences vs. patterns scoring many.
Parameters Z0-Z3 appears when this scoring scheme is used.

tree

a pattern is scored higher if it contains more information and/or
if it matches more diverse sequences. The sequence diversity is
calculated from a dendrogram which has to be input.

dist

similar to the tree scoring, except a matrix with pairwise the
similarity between all pairs of input sequences are used instead
of the tree. The matrix has to be input.

ppv

- a
measure of Positive Predictive Value - it is assumed that the
input sequences consitute a family, and are all contained in the
Swiss-Prot database. PPV measures how certain one can be that a
sequence belongs to the family given that it matches the pattern.

For the last three scoring schemes, an input file is needed and option SF
appears allowing the user to set his own file name.

Option X:

Exit the menu, and start the pattern discovery process.

Option Q:

Quit Pratt without searching for patterns.

Help Option:

Help is available on-line from the Pratt's menu. Just type
help option for help on a specific option from Pratt's
menu.

2.4 Controlling the search via command line options.

All parameters whose values can be set using the menu can also be set
from the command line. For parameters with numerical value (for
example CM (minimum number of sequences to match a pattern) the value
of this parameter is set by including -CM <value> in
the command line. If this is the only parameter for which you wish to use
a non-default value, your command line might look something likepratt fasta sequences -cm 20
if you wish to look for patterns matching minimum 20 of the sequences
in the file sequences (given in FastA format).

For parameters swithchin on or off options, you should include
on or off behind the option on the command line.
For example if you do not want pattern refinement to be done, your
command line might look likepratt fasta sequences -cm 20 -r off

Nomally if you set some parameters using the command line, Pratt will
just start the search using default values for the parameters that you
have not set. If you want to see the menu as well, include -menu
in the command line.

First run Pratt using a restrictive set of parameter values (for
example the default parameters). If it finds a pattern you're
happy with, then you're happy. If not, you can run Pratt again using
a less restrictive set of parameters, in one of the following ways:

allow for more ambiguous symbols: Increase B.

allow for longer gaps: Increase W.

allow for more flexibilities: Increase N, F, P.

decrease the minimum number of sequences to match a pattern -- decrease M.